Introduction

< Explain >

Goals

< what are you trying to achieve >

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Learn how to communicate with cbioportal and study what is available.

This portal is hierarchically structured. This is the workflow.
- Initiate cBioPortal API
- List studies
- List available datasets for the chosen study
  - Find all sample IDs associated with the dataset
  - Acquire clinical data
- List available molecular data associated with the dataset
- Download

Find you TCGA ID

Important here: you need to replace this with your own assigned TCGA ID. For this report I’m using TCGA-AR-A24T

Clinical data.

Now that we have a basic understanding of what is available lets go and download the actual data.

mutation table

Identifying pathogenic mutations. <— need to redo with mt from here onwards

Now that the data has been succesfully donwloaded and annotated lets study it a bit more.

Besides Mutation data we also downloaded expression RNAseq data in the form of TPM.

Here we review two types of very important pathway analysis.
- Gene set Enrichment Analysis ( GSEA )
- Over-Representation Analysis

demo only

Please see assignmet.
Figure out what figures to put and what to leave out.
know your myid and where it all fits.

RNAseq Volcano

Heatmap

GSEA summary1

GO 1

GO 2

mutations

CNA